wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions

Released 4 years ago, the Wallace EcoMod application (R package wallace) provided an open-source and interactive platform for modeling species niches and distributions that served as a reproducible toolbox and educational resource. wallace harnesses R package tools documented in the literature and makes them available via a graphical user interface that runs analyses and returns code to document and reproduce them. Since its release, feedback from users and partners helped identify key areas for advancement, leading to the development of wallace 2. Following the vision of growth by community expansion, the core development team engaged with collaborators and undertook a major restructuring of the application to enable: simplified addition of custom modules to expand methodological options, analyses for multiple species in the same session, improved metadata features, new database connections, and saving/loading sessions. wallace 2 features nine new modules and added functionalities that facilitate data acquisition from climate-simulation, botanical and paleontological databases; custom data inputs; model metadata tracking; and citations for R packages used (to promote documentation and give credit to developers). Three of these modules compose a new component for environmental space analyses (e.g., niche overlap). This expansion was paired with outreach to the biogeography and biodiversity communities, including international presentations and workshops that take advantage of the software's extensive guidance text. Additionally, the advances extend accessibility with a cloud-computing implementation and include a suite of comprehensive unit tests. The features in wallace 2 greatly improve its expandability, breadth of analyses, and reproducibility options, including the use of emerging metadata standards. The new architecture serves as an example for other modular software, especially those developed using the rapidly proliferating R package shiny, by showcasing straightforward module ingestion and unit testing. Importantly, wallace 2 sets the stage for future expansions, including those enabling biodiversity estimation and threat assessments for conservation.journal articl

Un informe y siete ensayos relacionados con la patrimonialización y la ciencia abierta en la Universidad de Antioquia 2017-2027

RESUMEN: Las reflexiones que se presentan a continuación, son el resultado del desarrollo de un proyecto denominado: «Aplicación web para la difusión de los patrimonios de la Universidad de Antioquia. Fase I: investigación, registro y ordenamiento de información», presentado y aprobado en el marco la Décima Cuarta Convocatoria Banco Universitario de Programas y Proyectos de Extensión —BUPPE— Culturas, Patrimonios y Creación Artística para la Transformación Social (2018); coofinanciado por el Museo Universitario — MUUA — y la Dirección de Regionalización de la Universidad de Antioquia, presentado con el objetivo principal de: […] obtener información detallada y suficiente para crear los contenidos de una aplicación web interactiva que presente y difunda los legados patrimoniales que alberga y salvaguarda la Universidad como aporte al conocimiento de la cultura y la historia del departamento y el país. Los objetivos del proyecto naturalmente retomaron las formulaciones que sobre el patrimonio circulan corrientemente en la Universidad y aparecían en el Portal Universitario; el periódico Alma Máter; la Agenda Cultural; los libros conmemorativos, especialmente los publicados a partir de la celebración de los 200 años de fundación de la Universidad, pero sobre todo, la cartilla publicada en 2015 titulada: «Patrimonio y memoria de tu Alma», ofrecida por el Museo Universitario como obsequio de fin de año a los profesores, se convirtió en acicate y justificación para participar en la convocatoria que permitió la realización del proyecto del que aquí se da cuenta.07 I. Informe 08 Presentación 16 El cómo y el qué del patrimonio hoy 38 El Plan de Desarrollo de la Universidad de Antioquia de cara al año 2027 39 La Universidad como patrimonio 43 Objetivos y compromisos institucionales del Plan de Desarrollo frente al patrimonio y la pragmática sobre la ciencia abierta 50 Acceso abierto 53 La transición hacia la ciencia abierta 58 Evaluación abierta 68 Los derechos de autor en el contexto colombiano 74 Las colecciones patrimoniales de la Universidad de Antioquia 76 El patrimonio, las colecciones patrimoniales universitarias ¿entre categorías clasificatorias divergentes? 96 Bibliografía II. Ensayos 105 Apuntes sobre patrimonialización en el contexto global. Los desafíos del patrimonio en un mundo en llamas / Daniel Sánchez Gómez 123 La arqueología como ciencia del patrimonio. Ensayo crítico sobre el propósito general de la disciplina / Daniel Grisales Betancur 144 Memorias y archivos literarios. Por los caminos de la tierra y el mundo / María Stella Girón López 169 Debates sobre bambuco y la emergencia fonográfica de la "música de carrilera" en el periodismo cultural colombiano en la década de 1950 / Lucas Mateo Guingue-Valencia 229 Medellín, una ciudad con muchas morales y pocas memorias / Guillermo Antonio Correa Montoya 252 Activación y consolidación de un patrimonio incómodo, construido sobre la memoria del narcotráfico y la violencia, en Medellín / Juan Diego Rojas Navarro y Darío Blanco Arboleda 276 Archivo, memoria y patrimonio. El caso del Fondo de Investigación y Documentación de Músicas Regionales de la Universidad de Antioquia / Valentina Rodríguez Góme

Operationalizing expert knowledge in species' range estimates using diverse data types

Estimates of species’ ranges can inform many aspects of biodiversity research and conservation-management decisions. Many practical applications need high-precision range estimates that are sufficiently reliable to use as input data in downstream applications. One solution has involved expert-generated maps that reflect on-the-ground field information and implicitly capture various processes that may limit a species’ geographic distribution. However, expert maps are often subjective and rarely reproducible. In contrast, species distribution models (SDMs) typically have finer resolution and are reproducible because of explicit links to data. Yet, SDMs can have higher uncertainty when data are sparse, which is an issue for most species. Also, SDMs often capture only a subset of the factors that determine species distributions (e.g., climate) and hence can require significant post-processing to better estimate species’ current realized distributions. Here, we demonstrate how expert knowledge, diverse data types, and SDMs can be used together in a transparent and reproducible modeling workflow. Specifically, we show how expert knowledge regarding species’ habitat use, elevation, biotic interactions, and environmental tolerances can be used to make and refine range estimates using SDMs and various data sources, including high-resolution remotely sensed products. This range-refinement approach is primed to use various data sources, including many with continuously improving spatial or temporal resolution. To facilitate such analyses, we compile a comprehensive suite of tools in a new R package, maskRangeR, and provide worked examples. These tools can facilitate a wide variety of basic and applied research that requires high-resolution maps of species’ current ranges, including quantifications of biodiversity and its change over time

wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions

Released 4 years ago, the Wallace EcoMod application (R package wallace) provided an open-source and interactive platform for modeling species niches and distributions that served as a reproducible toolbox and educational resource. wallace harnesses R package tools documented in the literature and makes them available via a graphical user interface that runs analyses and returns code to document and reproduce them. Since its release, feedback from users and partners helped identify key areas for advancement, leading to the development of wallace 2. Following the vision of growth by community expansion, the core development team engaged with collaborators and undertook a major restructuring of the application to enable: simplified addition of custom modules to expand methodological options, analyses for multiple species in the same session, improved metadata features, new database connections, and saving/loading sessions. wallace 2 features nine new modules and added functionalities that facilitate data acquisition from climate-simulation, botanical and paleontological databases; custom data inputs; model metadata tracking; and citations for R packages used (to promote documentation and give credit to developers). Three of these modules compose a new component for environmental space analyses (e.g., niche overlap). This expansion was paired with outreach to the biogeography and biodiversity communities, including international presentations and workshops that take advantage of the software's extensive guidance text. Additionally, the advances extend accessibility with a cloud-computing implementation and include a suite of comprehensive unit tests. The features in wallace 2 greatly improve its expandability, breadth of analyses, and reproducibility options, including the use of emerging metadata standards. The new architecture serves as an example for other modular software, especially those developed using the rapidly proliferating R package shiny, by showcasing straightforward module ingestion and unit testing. Importantly, wallace 2 sets the stage for future expansions, including those enabling biodiversity estimation and threat assessments for conservation.ISSN:0906-7590ISSN:1600-058